The recent development of high-throughput technologies and computational methods revealed the existence of many non-canonical short open reading frames (sORFs) on most prokaryotic and eukaryotic RNAs, including presumptive non-coding RNAs. Because of their short size (< 100 codons) and the use of alternative start codons and reading frames, these ubiquitous elements have been missed for long. Functional sORF-encoded peptides (sPEPs) have been demonstrated to be involved in a wide range of biological processes, including cell physiology and proliferation, signaling, organogenesis, cell growth and death, transport, enzymatic regulation, metabolism, development, cytoskeleton organization and major histocompatibility complex class-I (MHC-I) presentation. Some of them are even taking part in disease onset (e.g. cancers). Nonetheless, this novel class of peptides remains poorly characterized and annotation of most sPEPs is still missing. In addition, sORFs located upstream of the canonical ORFs of mRNAs (upstream ORFs, uORFs), have been early described as cis regulators of the translation. By changing the efficiency of the translation initiation at the canonical ORF, uORFs participate to the translational regulatory mechanism. Indeed, some uORFs have been shown to alleviate the repression of the protein synthesis of canonical ORFs under stress. However, existing models of regulation of the translation by uORFs are still limited to a few set of genes, and the mechanisms remain cryptic for most RNAs.

This project aims to investigate the sORFs functions by (i) identifying all sORFs in human genome, (ii) exploring sPEP functions in monocytes and (iii) exploring the mechanisms of regulation of the translation by the uORFs. Human monocytes constitute a good model as they are able to express MHC molecules, whilst numerous sPEPs have been determined to be presented as self-antigens. Monocytes are playing a major role in the initiation of immune responses and derived from a bone marrow progenitor common to dendritic cells. These last have special needs regarding their translational regulation and could thus constitute an interesting model to study sORFs cis-regulatory functions.

To address these questions, (i) publicly available data were gathered in a repository of unique sORFs identified by complementary methods, (ii) interactions of sPEPs with canonical proteins in monocytes were predicted to identify the processes targeted by sPEPs and (iii) ribosomes' behaviours were mimicked by implementing an agent-based model to identify the most important parameters for translational regulation by uORFs.

(i) By gathering publicly available sORF data, normalizing them and summarizing redundant information, a total of 664,771 unique sORFs were identified in human. This repository allows new analyses at locus, gene, transcript and ORF levels. (ii) Our findings suggest that sPEPs are involved in fundamental regulatory functions, both ubiquitous (protein, DNA and RNA metabolism, gene expression...) and related to specialized functions (immunological responses...). We also demonstrated that most sPEPs are preferentially interacting with annotated proteins of the same process as their cognate canonical protein. (iii) Finally, the agent-based model developed does not success yet to explain the mechanisms of translational regulation by the uORFs, but provides an adaptable tool to the scientific community for their investigation.

Keywords: short open reading frame (sORF), sORF-encoded peptide (sPEP), protein-protein interaction (PPI), translation

The manuscript of my PhD thesis is available on request.

Labs

• Theories and Approaches of Genomic Complexity (TAGC), Bioinformatics and genomics of molecular networks
• Centre d'Immunologie de Marseille Luminy (CIML), Dendritic cell biology

PhD programs

• Turing Centre for Living Systems (CENTURI), International PhD program (1st year group)
• Doctoral school of Life and health sciences (ED62) - Bioinformatics and Genomics, Aix-Marseille Université (AMU)

Accomplishments

• 3 publications + 2 manuscripts in preparation ( see publications section)
• 9+ participations to international and local conferences (oral talks and posters), including the International Conference on Systems Biology (ICSB, Berlin 2022)
• 250+ hours of training (creative thinking, oral and written communication, management, entrepreneurship, scientific winter and summer schools etc.)

Positions

• Co-representative of the PhD and master students at the TAGC lab council (2018-2019)
• Representative of the PhD students at the CENTURI education and steering committees (2018-2021)
• Member of the CENTURI team dedicated to the organization of tutored seminars (2018-2020)
• Member of the organization committee of the CENTURI PhD student & PostDoc scientific day (2020)
• Member of the organization committee of the CIML annual PhD workshop (2020)

Funding

• FRM "Espoirs de la recherche" grant - PhD fellowship (2021 - 2022)
• CENTURI PhD fellowship (2018 - 2021)

Please, feel free to contact me if you are willing to talk about my PhD project and the projects I am or have been involved in.